A Genome-Wide Association Study of Field and Seedling Response to Individual Stem Rust Pathogen Races Reveals Combinations of Race-Specific Genes in North American Spring Wheat

In recent years, leaf rust (LR) and stem rust (SR) have become a serious threat to bread wheat production in Kazakhstan. Most local cultivars are susceptible to these rusts, which has affected their yield and quality. The development of new cultivars with high productivity and LR and SR disease resistance, including using marker-assisted selection, is becoming an important priority in local breeding projects. Therefore, the search for key genetic factors controlling resistance in all plant stages, including the seedling stage, is of great significance. In this work, we applied a genome-wide association study (GWAS) approach using 212 local bread wheat accessions that were phenotyped for resistance to specific races of Puccinia triticina Eriks. (Pt) and Puccinia graminis f. sp. tritici (Pgt) at the seedling stages. The collection was genotyped using a 20 K Illumina iSelect SNP assay, and 11,150 polymorphic SNP markers were selected for the association mapping. Using a mixed linear model, we identified 11 quantitative trait loci (QTLs) for five out of six specific races of Pt and Pgt. The comparison of the results from this GWAS with those from previously published work showed that nine out of eleven QTLs for LR and SR resistance had been previously reported in a GWAS study at the adult plant stages of wheat growth. Therefore, it was assumed that these nine common identified QTLs were effective for all-stage resistance to LR and SR, and the two other QTLs appear to be novel QTLs. In addition, five out of these nine QTLs that had been identified earlier were found to be associated with yield components, suggesting that they may directly influence the field performance of bread wheat. The identified QTLs, including novel QTLs found in this study, may play an essential role in the breeding process for improving wheat resistance to LR and SR.

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Identification of Earliness Per Se Flowering Time Locus in Spring Wheat through a Genome-Wide Association Study

Crop Science ◽

10.2135/cropsci2016.01.0066 ◽

2016 ◽

Vol 56 (6) ◽

pp. 2962-2672 ◽

Cited By ~ 16

Author(s):

Sivakumar Sukumaran ◽

Marta S. Lopes ◽

Susanne Dreisigacker ◽

Laura E. Dixon ◽

Meluleki Zikhali ◽

...

Keyword(s):

Association Study ◽

Flowering Time ◽

Spring Wheat ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Earliness Per Se ◽

Genome Wide ◽

A Genome ◽

Per Se

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Genome‐wide Association Study of Agronomic Traits in a Spring‐Planted North American Elite Hard Red Spring Wheat Panel

Crop Science ◽

10.2135/cropsci2017.07.0423 ◽

2018 ◽

Vol 58 (5) ◽

pp. 1838-1852 ◽

Cited By ~ 8

Author(s):

Jayfred Godoy ◽

Shiferaw Gizaw ◽

Shiaoman Chao ◽

Nancy Blake ◽

Arron Carter ◽

...

Keyword(s):

Association Study ◽

Spring Wheat ◽

North American ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Genome Wide Association ◽

Hard Red Spring Wheat ◽

Genome Wide

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A Genome-Wide Association Study of Resistance to Stripe Rust (Puccinia striiformis f. sp. tritici) in a Worldwide Collection of Hexaploid Spring Wheat (Triticum aestivum L.)

G3 Genes|Genome|Genetics ◽

10.1534/g3.114.014563 ◽

2015 ◽

Vol 5 (3) ◽

pp. 449-465 ◽

Cited By ~ 118

Author(s):

Marco Maccaferri ◽

Junli Zhang ◽

Peter Bulli ◽

Zewdie Abate ◽

Shiaoman Chao ◽

...

Keyword(s):

Association Study ◽

Stripe Rust ◽

Spring Wheat ◽

Resistance Genes ◽

Genome Wide Association Study ◽

Puccinia Striiformis ◽

Infection Type ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

Abstract New races of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, show high virulence to previously deployed resistance genes and are responsible for large yield losses worldwide. To identify new sources of resistance we performed a genome-wide association study (GWAS) using a worldwide collection of 1000 spring wheat accessions. Adult plants were evaluated under field conditions in six environments in the western United States, and seedlings were tested with four Pst races. A single-nucleotide polymorphism (SNP) Infinium 9K-assay provided 4585 SNPs suitable for GWAS. High correlations among environments and high heritabilities were observed for stripe rust infection type and severity. Greater levels of Pst resistance were observed in a subpopulation from Southern Asia than in other groups. GWAS identified 97 loci that were significant for at least three environments, including 10 with an experiment-wise adjusted Bonferroni probability < 0.10. These 10 quantitative trait loci (QTL) explained 15% of the phenotypic variation in infection type, a percentage that increased to 45% when all QTL were considered. Three of these 10 QTL were mapped far from previously identified Pst resistance genes and QTL, and likely represent new resistance loci. The other seven QTL mapped close to known resistance genes and allelism tests will be required to test their relationships. In summary, this study provides an integrated view of stripe rust resistance resources in spring wheat and identifies new resistance loci that will be useful to diversify the current set of resistance genes deployed to control this devastating disease.

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The Genetic Architecture of Grain Yield in Spring Wheat Based on Genome-Wide Association Study

Frontiers in Genetics ◽

10.3389/fgene.2021.728472 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yuyao Li ◽

Jingquan Tang ◽

Wenlin Liu ◽

Wenyi Yan ◽

Yan Sun ◽

...

Keyword(s):

Grain Yield ◽

Association Study ◽

Spring Wheat ◽

Genetic Architecture ◽

Genome Wide Association Study ◽

Wheat Breeding ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

A Genome

Uncovering the genetic architecture for grain yield (GY)–related traits is important for wheat breeding. To detect stable loci for GY-related traits, a genome-wide association study (GWAS) was conducted in a diverse panel, which included 251 elite spring wheat accessions mainly from the Northeast of China. In total, 52,503 single nucleotide polymorphisms (SNPs) from the wheat 55 K SNP arrays were used. Thirty-eight loci for GY-related traits were detected and each explained 6.5–16.7% of the phenotypic variations among which 12 are at similar locations with the known genes or quantitative trait loci and 26 are likely to be new. Furthermore, six genes possibly involved in cell division, signal transduction, and plant development are candidate genes for GY-related traits. This study provides new insights into the genetic architecture of GY and the significantly associated SNPs and accessions with a larger number of favorable alleles could be used to further enhance GY in breeding.

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